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Computational models with thermodynamic and composition features improve siRNA design
BackgroundSmall interfering RNAs (siRNAs) have become an important tool in cell and molecular biology. Reliable design of siRNA molecules is essential for the needs of large functional genomicsExpand
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Comparison of approaches for rational siRNA design leading to a new efficient and transparent method
Current literature describes several methods for the design of efficient siRNAs with 19 perfectly matched base pairs and 2 nt overhangs. Using four independent databases totaling 3336 experimentallyExpand
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A periodic pattern of mRNA secondary structure created by the genetic code
Single-stranded mRNA molecules form secondary structures through complementary self-interactions. Several hypotheses have been proposed on the relationship between the nucleotide sequence, encodedExpand
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Expansion of the human μ-opioid receptor gene architecture: novel functional variants
The μ-opioid receptor (OPRM1) is the principal receptor target for both endogenous and exogenous opioid analgesics. There are substantial individual differences in human responses to painful stimuliExpand
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Comparative analysis of orthologous eukaryotic mRNAs: potential hidden functional signals.
Sequencing of multiple, nearly complete eukaryotic genomes creates opportunities for detecting previously unnoticed, subtle functional signals in non-coding regions. A genome-wide comparativeExpand
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Distinct Patterns of Expression and Evolution of Intronless and Intron-Containing Mammalian Genes
Comparison of expression levels and breadth and evolutionary rates of intronless and intron-containing mammalian genes shows that intronless genes are expressed at lower levels, tend to be tissueExpand
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Widespread positive selection in synonymous sites of mammalian genes.
Evolution of protein sequences is largely governed by purifying selection, with a small fraction of proteins evolving under positive selection. The evolution at synonymous positions in protein-codingExpand
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Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites.
The impact of synonymous nucleotide substitutions on fitness in mammals remains controversial. Despite some indications of selective constraint, synonymous sites are often assumed to be neutral, andExpand
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Selective constraint in intergenic regions of human and mouse genomes.
We aligned and analyzed 100 pairs of complete, orthologous intergenic regions from the human and mouse genomes (average length approximately 12 000 nucleotides). The alignments alternate betweenExpand
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Bioinformatical assay of human gene morbidity.
Only a fraction of eukaryotic genes affect the phenotype drastically. We compared 18 parameters in 1273 human morbid genes, known to cause diseases, and in the remaining 16 580 unambiguous humanExpand
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